[English] 日本語
Yorodumi
- PDB-8k0a: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k0a
TitleCryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex
Components
  • 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
  • 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
KeywordsBIOSYNTHETIC PROTEIN / 3-phenylpropionate/cinnamic acid dioxygenase
Function / homology
Function and homology information


3-phenylpropanoate dioxygenase / 3-phenylpropionate dioxygenase activity / 3-phenylpropionate dioxygenase complex / 3-phenylpropionate catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
3-phenylpropionate/cinnamic acid dioxygenase, alpha subunit / 3-phenylpropionate/cinnamic acid dioxygenase, beta subunit / Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. ...3-phenylpropionate/cinnamic acid dioxygenase, alpha subunit / 3-phenylpropionate/cinnamic acid dioxygenase, beta subunit / Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily
Similarity search - Domain/homology
3-phenylpropionate/cinnamic acid dioxygenase subunit alpha / 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Ma, L.X. / Xing, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex
Authors: Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q.
History
DepositionJul 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
B: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
C: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
D: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
E: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
F: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta


Theoretical massNumber of molelcules
Total (without water)215,3266
Polymers215,3266
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "A"
d_3ens_1chain "E"
d_1ens_2chain "D"
d_2ens_2chain "F"
d_3ens_2chain "B"

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1LYSLYSCC1 - 4531 - 453
d_2ens_1LYSLYSAA1 - 4531 - 453
d_3ens_1LYSLYSEE1 - 4531 - 453
d_1ens_2PHEPHEDD1 - 1721 - 172
d_2ens_2PHEPHEFF1 - 1721 - 172
d_3ens_2PHEPHEBB1 - 1721 - 172

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.500013409176, -0.866017661853, 1.88799150116E-6), (0.866017661825, -0.500013409139, 9.38847389141E-6), (-7.18656314089E-6, 6.32939682278E-6, 0.999999999954)321.78144284, 86.2267104389, -2.48626834889E-5
2given(-0.500017515201, 0.866015291139, -2.34426580397E-6), (-0.866015291117, -0.500017515163, 9.03294499064E-6), (6.65049452374E-6, 6.54680074184E-6, 0.999999999956)86.2285993224, 321.781594889, -0.0014687109586
3given(-0.500009991367, -0.866019635189, -1.02640280434E-6), (0.866019635189, -0.500009991368, 5.86775676288E-7), (-1.02137091445E-6, -5.95491281335E-7, 0.999999999999)321.781571807, 86.2274887472, 0.000201867813189
4given(-0.500011063374, 0.866019016248, 7.67216883869E-8), (-0.866019016248, -0.500011063374, -1.02970501069E-6), (-8.53382427394E-7, -5.81306338461E-7, 0.999999999999)86.2270488048, 321.782328396, 0.000180733286925

-
Components

#1: Protein 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha


Mass: 51166.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hcaE, digA, hcaA, hcaA1, phdC1, yfhU, b2538, JW2522
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0ABR5, 3-phenylpropanoate dioxygenase
#2: Protein 3-phenylpropionate/cinnamic acid dioxygenase subunit beta


Mass: 20609.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hcaF, digB, hcaA2, hcaB, phdC2, yfhV, b2539, JW2523
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q47140, 3-phenylpropanoate dioxygenase

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Homohexamer of inositol phosphate phosphatase SopB / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30478 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 52.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002815330
ELECTRON MICROSCOPYf_angle_d0.530520799
ELECTRON MICROSCOPYf_chiral_restr0.04462169
ELECTRON MICROSCOPYf_plane_restr0.0042736
ELECTRON MICROSCOPYf_dihedral_angle_d8.62862049
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints0.000596972794935
ens_1d_3CCELECTRON MICROSCOPYNCS constraints0.000640881405119
ens_2d_2DDELECTRON MICROSCOPYNCS constraints0.000577234944625
ens_2d_3DDELECTRON MICROSCOPYNCS constraints0.000581972372805

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more